title: Chromatin accessibility in C. albicans stimulated HoxER-PU.1 WT and HoxER-PU.1 KO neutrophils and DMSO, TSA or Entinostat treated  HoxER-PU.1 WT neutrophils

first: Frank

last: Rosenbauer

overall_design: Tn-Seq profiles of 2 hours C. albicans stimulated wildtype and PU.1 deleted neutrophils as well as DMSO, TSA or Entinostat treated  wildtype neutrophils were generated by deep sequencing in duplicates.

first: Josephine

last: Fischer

first: Carolin

last: Walter

first: Alexander

last: Tönges


title: Bacteria regulate B cell function in the gut

status: Public on Dec 31 2018

city: Uppsala

first: Haoyu

last: Liu

address: Husargatan 3

department: Medicinsk Cellbiologi, Avdelningen för Fysiologi

country: Sweden

institute: Uppsala Universuity

summary: B cell plays an important role in antibody induction response. We were aiming to describe two distinct B cell subpopulations in the intestinal lymphoid tissue ‘Peyer’s patches’ of mice, characterized by their transcriptional profile. B cells were sorted according to a combination of surface marker from wild type young mice, that were treated with bacteria for 7 days or control. RNA was extracted. Microarray analysis was then applied to identify the difference between two B cell subsets and the changes of expression within each B subset, due to treatment.

overall_design: To better understand the signaling events that separate BB and SB cells in PPs, four replicates of BB and SB from WT control mice or bacteria–treated mice were analyzed by whole-mouse genome microarray.

first: Tomas

last: Walden


title: SB28 genomic and expression analysis

status: Public on Feb 26 2019

city: Genève

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

country: Switzerland

institute: UNIGE

type: Expression profiling by high throughput sequencing

summary: Characterise this new cell line

overall_design: SB28 cell line: WES and RNA-seq

first: E

first: G

last: Vassilis

first: P

last: Walker


title: Transcriptomics profiling of CD141+ dendritic cells isolated from peripheral blood or synovial fluid of arthritis patients

status: Public on Dec 15 2018

city: la jolla

first: vipul

last: bhargava

state: California

address: 9500 gilman drive

country: USA

institute: ucsd

summary: Total RNA sequencing was performed on CD141+ DC isolated from peripheral blood of healthy individuals (n=4), synovial fluid of patients with inflammatory arthritis (n=5) and peripheral blood of patients with inflammatory arthritis (n=7). Cd1c+ DC were also sequenced from peripheral blood of healthy individuals (n=3).

overall_design: One RNA sample per subject was analyzed without replicates

first: Vipul

last: Bhargava

first: Mary

last: Canavan


title: Temporal auto-regulation during PU.1 locus SubTAD formation (ChIP-seq)

status: Public on Oct 15 2018

city: Münster

address: Robert-Koch-Str. 43

department: Institute of Molecular Tumor Biology

country: Germany

institute: University Hospital Münster

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetic control of gene expression occurs within discrete spatial chromosomal units called topologically associating domains (TADs), but the exact spatial requirements of most genes are unknown; this is of particular interest for genes involved in cancer. We therefore applied high-resolution chromosomal conformation capture-sequencing to map the three-dimensional (3D) organization of the human locus encoding the key myeloid transcription factor PU.1 in healthy monocytes and acute myeloid leukemia (AML) cells. We identified a dynamic ~75kb unit (SubTAD) as the genomic region in which spatial interactions between PU.1 gene regulatory elements occur during myeloid differentiation and are interrupted in AML. Within this SubTAD, proper initiation of the spatial chromosomal interactions requires PU.1 autoregulation and recruitment of the chromatin-adaptor protein LDB1 (LIM domain-binding protein 1). However, once these spatial interactions have occurred, LDB1 stabilizes them independently of PU.1 auto-regulation. Thus, our data support that PU.1 auto-regulates its expression in a ‘hit-and-run’ manner by initiating stable chromosomal loops that result in a transcriptionally active chromatin architecture.

overall_design: Study of 4 different cell types

first: Daniel

last: Schuetzmann

first: Martin

last: Dugas


title: Dynamic lipid mediator changes support infiltrating macrophage subtype transitions during skeletal muscle injury and regeneration

status: Public on Feb 01 2019

city: Debrecen

first: Nikolaos

last: Giannakis

address: Egyetem ter 1

department: Department of Biochemistry and Molecular  Biology

country: Hungary

institute: University of Debrecen

summary: Time-dependent profiles were recapitulated in sorted neutrophils and Ly6Chigh and Ly6Clow muscle macrophages, with a distinct pro-resolving signature observed in Ly6Clow reparative macrophages. RNA-seq analysis of macrophages stimulated with resolvin D2 (RvD2) showed similarities to transcriptional changes found during the temporal Ly6Chigh to Ly6Clow phenotypic transition. Importantly, RvD2 promoted the temporal progression from Ly6Chigh to Ly6Clow macrophages in vivo.

overall_design: Total RNA was isolated with TRIZOL reagent according to the manufacturer’s recommendation. 20ug glycogen (Ambion) was added as carrier for RNA ethanol precipitation.

first: Laszlo

last: Nagy

first: Nikolas

first: Andreas

last: Patsalos


title: Temporal auto-regulation during PU.1 locus SubTAD formation (4C-seq)

first: Frank

last: Rosenbauer

summary: Epigenetic control of gene expression occurs through discrete spatial chromosomal units called topologically associating domains (TADs), but the exact spatial requirements of most genes are unknown; this is of particular interest for genes involved in disease. We therefore applied high-resolution chromosomal conformation capture-sequencing to map the three-dimensional (3D) organization of the locus encoding the key myeloid transcription factor PU.1 in healthy monocytes and acute myeloid leukemia (AML) cells. We identified a dynamic ~75kb unit (SubTAD) as the genomic region in which spatial interactions between PU.1 gene regulatory elements occur during myeloid differentiation and are interrupted in AML. Within this SubTAD, initiating the spatial chromosomal interactions requires PU.1 auto-regulation and recruitment of the chromatin-adaptor protein LDB1 (LIM domain-binding protein 1). However, once formed, this SubTAD remains stable even when auto-regulation is impaired. Thus, our data support that PU.1 auto-regulation functions in a ‘hit-and-run’ manner, whereby it organizes chromosomal loops to create a transcriptionally active chromatin architecture.

overall_design: Study of 5 different cell types.

first: Carolin


title: Expression profiling of Pseudomonas aeruginosa in chronic wound exudate media

status: Public on Oct 03 2018

city: Bozeman

first: Kerry

middle: S

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

institute: Montana State University

summary: Transcriptomic, metabolomic, physiological, and computational modeling approaches were integrated to gain insight into the mechanisms of antibiotic tolerance in an in vitro biofilm system. Pseudomonas aeruginosa biofilms were grown in drip-flow reactors on a medium composed to mimic the exudate from a chronic wound (CWE).  After 72 hours, the biofilms were treated with CWE (control biofilms) or CWE containing ciprofloxacin (treated biofilms) for an additional 24 hours. Planktonic samples were cultivated to early logarithmic phase in CWE. The biofilm specific growth rate was estimated via elemental balances to be approximately 0.37 h-1, or one-third of the planktonic maximum specific growth rate.  Global analysis of gene expression indicated decreased anabolic activity in biofilms compared to planktonic cells.  A focused transcriptomic analysis revealed the induction of multiple stress responses in biofilm cells, including those associated with growth arrest, zinc limitation, hypoxia, and acyl-homoserine lactone quorum sensing.

overall_design: Three biological replicates were prepared and analyzed for the following three growth conditions: (1)Pseudomonas aeruginosa was grown planktonically to early log phase. (2) Pseudomonas aeruginosa was grown in drip flow biofilm reactors on hydroxyapetite-coated glass slides for four days. (3) Pseudomonas aeruginosa was grown in drip flow biofilm reactors on hydroxyapetite-coated glass slides for three days and then treated with 1 mg/ml ciprofloxacin for an additional day.

first: Philip

last: Stewart

first: Ben

last: White

first: Laura

last: Boegli

first: Timothy

last: Hamerly

first: Michael

middle: J

last: Franklin

first: Brian

last: Bothner

first: Garth

middle: A

last: James

first: Steve

last: Fisher

first: Francisco

middle: G

last: Vital-Lopez

first: Anders

last: Wallqvist


title: Shared and distinct transcriptomic cell types across neocortical areas

status: Public on Oct 31 2018

city: Seattle

first: Allen

last: Institute

state: WA

address: 615 Westlake Ave N

institute: The Allen Institute for Brain Science

summary: Neocortex contains a multitude of cell types segregated into layers and functionally distinct regions. To investigate the diversity of cell types across the mouse neocortex, we analyzed 12,714 cells from the primary visual cortex (VISp), and 9,035 cells from the anterior lateral motor cortex (ALM) by deep single-cell RNA-sequencing (scRNA-seq), identifying 116 transcriptomic cell types. These two regions represent distant poles of the neocortex and perform distinct functions. We define 50 inhibitory transcriptomic cell types, all of which are shared across both cortical regions. In contrast, 49 of 52 excitatory transcriptomic types were found in either VISp or ALM, with only three present in both. By combining single cell RNA-seq and retrograde labeling, we demonstrate correspondence between excitatory transcriptomic types and their region-specific long-range target specificity. This study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct regions of the mouse cortex.

overall_design:
scRNA-seq of 25,481 single cells from two regions of adult Mouse cortex: anterior lateral motor cortex (ALM) and primary visual cortex (VISp) and 2,986 control samples

Please note that the current records represent 232-grouped sample records (i.e. 28706-samples collaped into 232-logical groups) and the complete metadata for each single sample is provided as 'complete_metadata_28706-cells.csv'.

The file 'accession_table.csv' provides all of the GEO and SRA IDs along with the sample_name/title that matches the metadata.

first: Bosiljka

last: Tasic

first: Zizhen

last: Yao

first: Kimberly

last: Smith

first: Lucas

middle: T

last: Graybuck

first: Thuc

middle: N

last: Nguyen

first: Darren

last: Bertagnolli

first: Jeff

last: Goldy

first: Emma

last: Garren

last: Economo

first: Sarada

last: Viswanathan

first: Osnat

last: Penn

first: Trygve

last: Bakken

first: Jeremy

last: Miller

first: Olivia

last: Fong

first: Karla

middle: E

last: Hirokawa

first: Kana

last: Lathia

first: Christine

last: Rimorin

last: Tieu

first: Rachael

last: Larsen

first: Tamara

last: Casper

first: Eliza

last: Barkan

first: Matthew

last: Kroll

first: Seana

last: Parry

first: Nadiya

middle: V

last: Shapovalova

first: Daniel

last: Hirchstein

first: Julie

last: Pendergraft

first: Tae

middle: K

last: Kim

first: Aaron

last: Szafer

first: Nick

last: Dee

first: Peter

last: Groblewski

first: Ian

last: Wickersham

first: Ali

last: Cetin

last: Harris

first: Boaz

middle: P

last: Levi

first: Susan

middle: M

last: Sunkin

first: Linda

last: Madisen

first: Tanya

middle: L

last: Daigle

first: Loren

last: Looger

first: Amy

last: Bernard

first: John

last: Phillips

first: Ed


title: Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes

status: Public on Dec 19 2018

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Oocyte growth is a key step in forming mature eggs that are ready to be fertilized. The states and modifications of chromatin represent critical sources of information for this process. However, the dynamics and interrelations of these chromatin characteristics remain elusive. In this study, we developed an improved scCOOL-seq technique (iscCOOL-seq), which is a multi- omics, single-cell and single-base resolution method with high mapping rates, and explored the chromatin accessibility landscape and its relationship to DNA methylation in growing mouse oocytes. The most dramatic change in chromatin accessibility occurs during oocyte growth initiation, accompanied with prominent transcriptome alterations and an elevated variation in DNA methylation levels among individual oocytes. Unlike CpG islands (CGIs), partially methylated domains (PMDs) are associated with a low density of nucleosome-depleted regions (NDRs) during the whole maturation period. Surprisingly, highly expressed genes are usually associated with NDRs at their transcriptional end sites (TESs). In addition, genes with de novo methylated gene bodies during oocyte maturation are already open at their promoters before oocyte growth initiation. Furthermore, epigenetic and transcription factors that might be involved in oocyte maturation are identified. Our work paves the way for dissecting the complex, yet highly coordinated, epigenetic alterations during mouse oocyte growth and the establishment of totipotency.

overall_design: Four scRNA-seq (296 cells in total) and 734 iscCOOL-seq of mouse oocytes as well as 40 mouse ESCs were performed.

first: Chan

last: Gu


title: RNAseq quantitative analysis of naïve wild type and interleukin-6 knockout mice

status: Public on Oct 01 2018

city: Nashville

first: Lauren

middle: Katie

last: Wareham

state: Tennessee

address: 2213 Garland Avenue, MRBIV 11435a

department: Vanderbilt Eye Institute

institute: Vanderbilt University Medical Center

summary: The purpose of this study was to investigate general trasncriptomic changes in wild type and interleukin-6 knockout mice

overall_design: Retinal mRNA profiles of naive mice were generated by 100 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000).

first: Rebecca

last: Sappington


title: Whole genome cardiac gene expression profiling of transgenic mice with myocardium-specific expression of RKIP (PEBP1), kinase-inactive GRK2-K220R (ADRBK1-K220R), SCD1, and UCP1

status: Public on Sep 18 2018

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

institute: ETH Zurich

summary: The raf kinase inhibitor protein, RKIP, is up-regulated on cadiac biopsy specimens of heart failure patients. To investigate the in vivo role of an increased cardiac content of RKIP, we generated transgenic mice with myocardium-specific expression of RKIP (PEBP1; phosphatidylethanolamine binding protein 1) under control of the alpha-MHC promoter in B6 (C57BL/6J) background. Because RKIP is a dual-specific GRK2 and Raf kinase inhibitor, RKIP-transgenic mice were compared to transgenic mice with myocardium-specific expression of the GRK2 inhibitor, GRK2-K220R, which is a kinase-inactive GRK2 (ADRBK1) mutant with dominant-negative function. In frame of our studies, we found that RKIP-transgenic mice developed signs of heart failure and cardiotoxic lipid load at an age of 8 months. In contrast, transgenic expression of GRK2-K220R improved cardiac function and protected against chronic pressure overload-induced symptoms of heart failure. To identify genes related to cardiotoxic lipid load, we further determined the cardiac gene expression profile of Tg-SCD1 mice with mypcardium-specific expression of SCD1 (stearoyl-CoA desaturase-1) and Tg-UCP1 mice with heart-specific expression of UCP1 (uncoupling protein 1).

overall_design: Whole genome microarray gene expression profiling was performed of hearts from aged, 8-month-old Tg-RKIP mice, Tg-GRK2-K220R mice, Tg-SCD1 mice, and Tg-UCP1 mice. All transgenic mice had B6 background, and the control group consisted of age-matched non-transgenic B6 mice. Two biological replicates were made of each group, and total cardiac RNA of three mice was pooled for one gene chip.

first: Joshua

last: Abd Alla


title: Genomic profiling in eWAT, iWAT, and BAT-derived adipocytes

status: Public on Nov 13 2018

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Examination of PPARg occupancy (GSE41481) and DNA hypersensitive sites (GSE122453) in in vitro differentiatied adipocytes isolated from epididymal and inguinal white adipose tissues, as well as brown adipose tissue.

overall_design: Refer to individual Series


title: Genome-wide DNA methylation mapping of primary human uterine leiomayoma and myometrium cells by MethylCap-seq

status: Public on Jan 01 2019

city: Chicago

first: Shimeng

last: Liu

state: Illinois

address: 320 East Superior Street

institute: Northwestern University

summary:
Purpose: To investigate the role of DNA methylation in human uterine leiomyoma tumorigenesis, we profiled genome-wide DNA methylation patterns of  leiomyoma cells (LM) and adjacent normal myometrial cells (MM) treated with or without DNA methylation inhibitor 5-Aza.
Methods:  Primary cells were isolated from fresh uterine myometrium or leiomyoma tissue. Cells were treated with vehicle (DMSO) or 5 µM 5’-aza for 96h with medium refreshed every 24h. Genomic DNA was extracted from LM and MM cells using DNeasy Blood and Tissue Kit (Qiagen, 69504) and fragmented to 300-500bp using Covaris M220. Methylated DNA fragments were captured using the MethylCap Kit (Diagenode, C02020010). Next-generation sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems, KK8502) and KAPA Single-Indexed Adapter Kit (KAPA Biosystems, KK8710). Libraries were sequenced under 75bp paired-end sequencing format. Sequences were aligned to the hg19 reference genome using Bowtie2. Histone style peak calling, differential binding analysis (getDifferentialPeaks) and motif analysis were performed using Homer under default settings. Differentily methylated regions (DMRs) were detected with a fold enrichment over background tag count ≥4 and poisson enrichment p-value over background tag count <0.0001. Differential DNA methylation between MM and LM (with or without treatment) at select regions were validated through qPCR.
Results: More than 100,000 methyalted regions were detected in each sample. We discovered 21,086 DMRs between MM and LM cells under basal (vehicle treated) condition. In cells treated with 5-aza, we detected 8811 DMRs between MM and LM. We compared the genomic context of DMRs identified by MethylCap-Seq with the probe distribution of the HM450 array and detected large differences between these two methods. For example, 44.23% of DMR were located in intergenic regions by MethylCap-Seq, which was drastically higher than the percentage of HM450 array probes located in intergenic regions  Downstream network enrichment analysis and motif analysis indicated that DMR-associated genes and regions are crucial for the tumor progression and hormone responsiveness of LM.
Conclusions: Our study represents the detailed analysis of differential DNA methyaltion profiles between MM and LM using MethylCap-seq. Our results showed a more comprehensive evaluation of DNA methyaltion landscapes of MM and LM compared with previous array based analysis. We conclude that DNA methylation plays a crucial role in hormone-dependent LM tumorigenesis.

overall_design: Genome-wide DNA methylation mapping of primary human uterine leiomayoma and myometrium cells with or without DNA methylation inhibitor 5-Aza treatment using MethylCap-Seq

first: Ping

last: Yin


title: RNAseq of wild type zebrafish germline (ovary, oocyte, testis)

status: Public on Sep 07 2018

city: Vienna

first: Andrea

last: Pauli

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Goal of this study is the gene expression analysis of the zebrafish adult germline (ovary, oocyte, testis)

overall_design: Three tissue types (ovary, oocyte, testis) from adult wildtype (TLAB) zebrafish; two replicates each

first: Luis

last: Cabrera Quio

first: James

last: Gagnon

first: Alexander

middle: F

last: Schier


title: Single cell RNA sequencing of cultured CCR10+ and CCR10- lung airway epithelial cells

status: Public on Sep 04 2018

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: Mechanically dissociated IPF lung explant derived cellular suspensions were cultured in 50% senescent lung fibroblast conditioned medium + 50% fibroblast complete medium (DMEM + 15% FBS + antiboitics) and 10 µM of Y27632. After approximately 2 weeks, cells were passaged and cultured overnight in Pneumacult Ex Plus medium (STEMCELL technologies).

overall_design: Explanted IPF lung tissues were mechanically minced to release loosely adherent and non-adherent cells. Cells were purified by passing the dissociated suspensions through a sterile 100 µm filter and then cultured in CRC medium: 50% senescent lung fibroblast conditioned medium + 50% fibroblast complete medium (DMEM + 15% FBS + antiboitics) and 10 µM of Y27632. Medium was changed every 3 days for approximately two weeks. After two weeks, cells were dissociated using Accutase solution and replated in PnemaCult Ex Plus medium (STEMCELL technologies) containing 10 µM Y27632 overnight. The next morning epithelial cells were dissociated using Accutase solution, stained with anti-EpCAM and -CCR10 antibodies and EpCAM+ CCR10+ and EpCAM+ CCR10- epithelial cells were FACS sorted using a BD Aria III sorter. Single sorted cells were then caputred and sequenced using 10x genomics platform.


title: Med23 serves as a gatekeeper of the myeloid potential of hematopoietic stem cells

status: Public on Jul 14 2018

summary: In response to myeloablative stresses, HSCs are rapidly activated to replenish myeloid progenitors, while maintaining full potential of self-renewal to ensure life-long hematopoiesis. However, the key factors that orchestrate HSC activities during physiological stresses remain largely unknown. Here we report that Med23 controls the myeloid potential of activated HSCs. Ablation of Med23 in hematopoietic system leads to lymphocytopenia. Med23- deficient HSCs undergo myeloid-biased differentiation and lose the self-renewal capacity. Interestingly, Med23-deficient HSCs are much easier to be activated in response to physio- logical stresses. Mechanistically, Med23 plays essential roles in maintaining stemness genes expression and suppressing myeloid lineage genes expression. Med23 is downregulated in HSCs and Med23 deletion results in better survival under myeloablative stress. Altogether, our findings identify Med23 as a gatekeeper of myeloid potential of HSCs, thus providing unique insights into the relationship among Med23-mediated transcriptional regulations, the myeloid potential of HSCs and HSC activation upon stresses.

overall_design: Hematopoietic stem cells in the bone marrow were isolated from WT or Med23-dificient adult mice, and were subjected to scRNA-seq.

first: Xufeng

last: Chen

first: Jingyao

last: Zhao

first: Xiaolong


title: Human Huntington’s Disease iPSC-derived cortical neurons display altered transcriptomics, morphology and electrophysiological maturation

status: Public on Sep 29 2018

summary: Huntington's disease (HD) is a neurodegenerative disease caused by an expanded CAG repeat in the Huntingtin (HTT) gene. Induced pluripotent stem cell (iPSC) models of HD provide an opportunity to study the mechanisms underlying disease pathology in patient tissues relevant to disease. Murine studies have demonstrated that HTT is intricately involved in corticogenesis, and mutant (mt) HTT cannot compensate for the loss of non-CAG-expanded HTT. However, the critical effect of mtHTT in human corticogenesis has not yet been specifically explored and due to inherent differences in cortical development and timing between humans and mice. We therefore differentiated HD and non-diseased iPSCs into functional cortical neurons. While HD patient iPSCs can be successfully differentiated towards a cortical fate in culture, the resulting neurons display transcriptomic, morphological and functional phenotypes indicative of altered neurodevelopment. This is the first demonstration of altered corticogenesis from HD human patient cells, further supporting the potential neurodevelopmental aspect of HD.

overall_design: HD patients with an expanded CAG HTT allele of 180 (CS97iHD180n), 109 (CS09iHD109n), or 77 CAG repeats (CS77iHD77n) and from three non-HD “controls” with 33 (CS83iCTR33n), 21 (CS00iCTR21n), or 18 (CS25iCTR18n) repeat CAG alleles. iPSCs were differentiated towards a cortical fate as described in Shi et al. (doi: 10.1038/nprot.2012.116.) for 0 (iPSC colonies), 60, 80, 100, 130 days.

first: Shagun

last: Mehta

first: Colton

last: Tom

first: Yizhou

last: Wang

first: Catherine

last: Bresee

first: David

last: Rushton

first: Pranav

last: Mathkar

first: Jie

last: Tang

first: Virginia

middle: B

last: Mattis


title: Benchmarking of 4C-seq pipelines based on real and simulated data

status: Public on May 29 2019

first: Frank

last: Rosenbauer

type:
Other
Third-party reanalysis

summary: With its capacity for high-resolution data output in one region of interest, chromosome conformation capture combined with high-throughput sequencing (4C-seq) is a state-of-the-art next-generation sequencing technique that provides epigenetic insights, and regularly advances current medical research. However, 4C-seq data is complex and prone to biases, and while specialized programs exist, an unbiased, extensive benchmarking is still lacking. Furthermore, neither substantial datasets with fully characterized ground truth, nor simulation programs for realistic 4C-seq data have been published. We conducted a benchmarking study on 54 4C-seq samples from 12 datasets, including original murine BMM, T-cell, and 416B data, and developed a novel 4C-seq simulation software to allow for more detailed comparisons of 4C-seq algorithms on 50 simulated datasets with 10 to 120 samples each.

sample_organism:
Homo sapiens
Mus musculus

overall_design: 54 4C-seq samples from 12 datasets, including original murine BMM, T-cell, and 416B data. Re-analyzed samples are from GSE77265, GSE87299, SRP023622, GSE111863, GSE52595, SRA048225, GSE52457, PRJEB5236, GSE62269, GSE101423, and GSE96546. The processed data for these re-analyzed samples are available in a tar archive at the foot of this page.

first: Carolin

last: Walter

first: Daniel

last: Schuetzmann

first: Martin

last: Dugas


title: RNA polymerase mapping in plants identifies enhancers enriched in causal variants

status: Public on Jun 21 2018

city: Ithaca

first: Roberto

last: Lozano

state: NY

address: 358 Plant Science Building, Cornell University

department: Plant Breeding and Genetics

institute: Cornell University

summary: Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have been reported to be absent in plants based on a study of Arabidopsis thaliana. Here, our PRO-Seq analysis in cassava (Manihot esculenta) identified peaks of transcriptionally-engaged RNA polymerase II (Pol2) at both 5’ and 3’ ends of genes, consistent with paused or slowly-moving Pol2, and divergent transcription at potential intragenic enhancers.  A full genome search for bi-directional transcription using an algorithm for enhancer detection developed in mammals (dREG) identified many enhancer candidates. These sites show distinct patterns of methylation and nucleotide variation based on genomic evolutionary rate profiling characteristic of active enhancers.  Maize GRO-Seq data showed RNA polymerase occupancy at promoters and enhancers consistent with cassava but not Arabidopsis. Furthermore, putative enhancers in maize identified by dREG significantly overlapped with sites previously identified on the basis of open chromatin, histone marks, and methylation. As evidence of the functional relevance of these sites in cassava, we show that SNPs in them predict significantly more variation in fitness and root composition than SNPs in chromosomal segments randomly ascertained from the same intergenic distribution. The findings shed new light on plant transcription regulation and its impact on development and plasticity.

sample_organism:
Manihot esculenta
Zea mays

platform_organism:
Manihot esculenta
Zea mays

overall_design: Nascent RNA profiling of seedling from two different plant species (Maize and Cassava)

first: Gregory

last: Booth

first: Bilan

middle: Y

last: Omar

first: Bo

last: Li

first: Edward

last: Buckler

first: John

last: Lis

first: Jean-Luc

last: Jannink

first: Dunia

last: Pino del Carpio


title: The cAMP inducible Coactivator CRTC3 Attenuates Brown Adipose Tissue Thermogenesis

status: Public on May 28 2018

city: San Diego

first: Ezra

last: Wiater

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

summary: CRTC3 deficiency in brown fat regulates brown fat function

overall_design: 4 day differentiated primary mouse SVF cells from Brown fat of wild-type or CRTC3 BKO mice treated or not with Forskolin (FSK), which activates the hormone adenylate cyclase. This compound is added to cell culture media to activate the PKA pathway.

first: Young-Sil

last: Yoon

first: Wen-Wei

last: Tsai

first: Sam

last: Vandevelde

first: Zhijiang

last: Chen

first: Kuo

last: Lee

first: Donald

last: Morgan

first: Kamal

last: Rhamouni

first: Shigenobu

last: Matsumura

first: Youngsup

last: Song

first: Marc

last: Montminy


title: Regulatory network controlling tumor-promoting inflammation in human cancers [RNA-seq]

status: Public on Jun 11 2018

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

summary: Using an inducible, inflammatory model of breast cellular transformation, we describe the transcriptional regulatory network mediated by STAT3, NF-kB, and AP-1 factors on a genomic scale.  These regulators form transcriptional complexes that directly regulate the expression of hundreds of genes in oncogenic pathways, such as cell proliferation, metastasis, angiogenesis, apoptosis and metabolism, via a positive feedback loop.  This inflammatory feedback loop and associated network, which function to various extents in many types of cancer cells and patient tumors, is the basis for an “inflammation” index that defines cancer types by functional criteria.  The inflammation index is negatively correlated with expression of genes involved in DNA metabolism, and transformation is associated with genome instability.  Inflammatory tumors are preferentially associated with infiltration immune cells that might be recruited to the site of the tumor via inflammatory molecules produced by the cancer cells.

overall_design: RNA-seq during MCF10A-ER-Src cell transformation and after STAT3, NF-kb, JUN, JUNB and FOS knockouts

first: He

last: Lizhi

first: Ji

last: Zhe

first: Kevin

last: Struhl


title: Regulatory network controlling tumor-promoting inflammation in human cancers

summary: This SuperSeries is composed of the SubSeries listed below.


title: Isolation and molecular characterization of amniotic fluid-derived mesenchymal stem cells obtained from Caesarean sections

status: Public on Jan 12 2018

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: Human amniotic fluid cells (AFCs) are immune-privileged with low immunogenicity and anti-inflammatory properties. Furthermore, they are high proliferative and have a broad differentiation potential, making them amenable for cell replacement therapies. Amniotic fluid (AF) is routinely obtained via amniocentesis. It contains heterogeneous populations of foetal-derived differentiated and undifferentiated progenitor cells including mesenchymal stem cells (MSCs). AF-derived mesenchymal stem cells (AF-MSCs) can self-renew and have a high proliferation and differentiation potential. In this study, we isolated AFCs from AF obtained during Caesarean sections (C-sections) and characterized them. The AFCs showed typical MSCs characteristics in relation to morphology, in vitro differentiation potential, cell surface marker expression and secreted factors. Subpopulations of AF-MSCs expressed several pluripotency-associated markers such as stage specific embryonic antigen 4 (SSEA4), c-Kit, TRA-1-60 and TRA-1-81, making them reprogrammable to induced pluripotent stem cells (iPSCs) without the use of ectopic gene expression. Additionally, they express the mesenchymal marker - Vimentin and multipotency-associated stem cell marker - CD133. Furthermore, the transcriptome and secretome analyses showed significant overlap with bone marrow-derived MSCs. C-section-derived AFMSCs can be routinely obtained without any risk to the foetus. Patient-specific AF-MSCs can be used for personalized cell therapies and disease modelling.

overall_design: The transcriptomes of human AF-MSCs from C-sections were compared to human fetal MSCs as well as human pluripotent cells (H1, H9, B4) by microarray analysis (PrimeView Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Lucas

last: Spitzhorn


title: Temporal auto-regulation during PU.1 locus SubTAD formation

status: Public on Oct 15 2018

first: Frank

last: Rosenbauer


title: Deciphering a secondary genetic code in neurons: the role of codon bias in regulating neuronal protein levels and implications for Elongator-mediated neurological disease

status: Public on Apr 25 2018

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Familial dysautonomia (FD) results from mutation in IKBKAP/ELP1, a gene encoding the scaffolding protein for the Elongator complex. This highly conserved complex is required for the translation of codon-biased genes in lower organisms. Here we investigate whether Elongator serves a similar function in mammalian peripheral neurons, the population devastated in FD. Using codon-biased eGFP sensors, and multiplexing of codon usage with transcriptome and proteome analyses of over 6,000 genes, we identify two categories of genes, as well as specific gene identities that depend on Elongator for normal expression. Moreover, we show that multiple genes in the DNA damage repair pathway are codon-biased, and that with Elongator loss, their misregulation is correlated with elevated levels of DNA damage. These findings link Elongator's function in the translation of codon-biased genes with both the developmental and neurodegenerative phenotypes of FD, and also clarify the increased risk of cancer associated with the disease.

overall_design: Examining the major genetic pathways that require IKAP are hampered by that Ikbkap null mice are embryonic lethal (E10), but can be examined by genome-wide transcriptome analysis of the dorsal root ganglia from Wnt1-Cre;IkbkapLoxP/LoxP E17.5 fetuses (Ikbkap is deleted from the neural crest). Mice homozygous for a floxed allele of Ikbkap (exon 4) were crossed to mice that are heterozygous for this floxed allele and a Wnt1-Cre transgene. Dorsal root ganglia were removed from E17-18 Wnt1-Cre;IkbkapLoxP/LoxP embryos and stored at -80 until RNA was isolated. Five wildtype and three conditional knock-out animals were analyzed for this experiment.

first: Joy

last: Goffena

first: Frances

last: Lefcort

first: Yongqing

last: Zhang

first: Elin

last: Lehrmann

first: Marta

last: Chaverra

first: Jehremy

last: Felig

first: Richard

last: Buksch

last: Becker

first: Lynn

last: George


title: Transcriptome analyses of the nervous system of Familial Dysautonomia-model mice identify novel cellular pathways dependent on Ikbkap/Elp1

status: Public on Apr 26 2018


title: Regulatory network controlling tumor-promoting inflammation in human cancers [ChIP-seq]

last: Ji

overall_design: ChIP-seq for STAT3, NF-kb, JUN, JUNB and FOS before and after MCF10A-ER-Src cell transformation

first: Joseph

middle: D

last: Fleming


title: Evidence for functional interactions between the placenta and brain in pregnant mice

status: Public on Oct 26 2018

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

summary: In this study, we profiled gene expression of maternal brain, fetal brain and placenta at day 15 of pregnancy to investigate global crosstalk of genes between placenta and brain in mice .

overall_design: Total RNA was sequenced from placenta, maternal brain and fetal brain from wildtype mice at day 15 pregnancy. Also,  total RNA was sequenced from placenta of FOXA2 conditional (uterine) knockout mice for comparsion with  gene expression of control wildtype mice at the same day (day 15) of pregnancy.

first: Andrew

last: Kelleher

first: Thomas

last: Spencer


title: LPAR signaling activated in neural crest stem cells promotes melanoma cell growth, invasion and therapy resistance

status: Public on Dec 01 2017

city: Philadelphia

first: Jianglan

last: Liu

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute


title: Identification of a distinct IL-10 producing subset of innate lymphoid type-2 effector cells with regulatory potential

status: Public on Nov 13 2017

first: AGCT

last: Core

summary: ILC210 represent a distinct effector population of ILC2 cells that have regulatory potential

overall_design: comparison between ILC2 cells with IL-33 stimulation or not on transcriptome change

first: Corey

middle: R

last: Seehus

first: Asha

last: Kadavallore

first: Brian

last: de la Torre

first: Yizhou

last: Wang

first: Jie

last: Tang

first: Jonathan

last: Kaye


title: LPAR signaling activated in neural crest stem cells promotes melanoma cell growth, invasion and therapy resistance [HumanWG6_V2]

summary: To pinpoint developmental pathways that are up-regulated both in neural crest stem cells (NCSC) and in melanoma cells but not in melanocytes, we carried out computational analyses to compare gene expression profiles of human skin-derived NCSC, epidermal melanocytes and melanoma cells. Our aim was to preselect genes that exhibit high mRNA expression levels both in melanoma cells and in NCSC but low levels in melanocytes.

overall_design: The microarray data were generated in our laboratory from six melanoma cell lines, six NCSC samples and four melanocyte samples.

first: Liu

last: Jianglan


title: LPAR signaling activated in neural crest stem cells promotes melanoma cell growth, invasion and therapy resistance [HumanHT-12 V4.0]

summary: LPAR1 (lysophosphatidic acid receptor 1) is identified in targeted siRNA screens which is required for the survival and maintenance of nueral crest stem cells (NCSC) as well as the growth and invasion of melanoma cells. To gain mechanistic insights into how LPAR signaling modulates melanoma cell growth, We conducted an Illumina genome-wide gene expression microarray experiment to profile melanoma cells treated with the autotaxin inhibitor, HA130. Melanoma cells treated with vehicle control,DMSO is included as a control.

overall_design: The analysis was done in melanoma cell line, WM9, treated with DMSO or HA130.


title: Regulation of Angiotensin II Actions by Enhancers and Super-enhancers in Vascular Smooth Muscle Cells

status: Public on Dec 25 2017

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: We have profiled Ang II regulated enhancer and super-enhancers in Rat Vascular smooth muscle cells using genomewide analysis of enhancer marks H3K27ac, H3K4me1 and super-enhancer mark BRD4.

overall_design:
Examined two enhancer mark H3K4me1 and H3k27ac and superenhancer mark BRD4 in Rat Vascular smooth muscle cells with or without Ang II

Please note that the sample processing especially data processing is different between the two datasets (H3K4me1/H3k27ac vs. BRD4).

first: Rama

last: Natarajan

first: Sadhan

last: Das

first: Zhuo

first: Parijat

last: Senapati


title: Transcriptome analysis of Blimp1-sufficient (Ctrl) and Blimp1-deficient (CKO) CD4+ Foxp3+ regulatory (Treg) and Foxp3- effector (Teff) T cells

status: Public on Sep 14 2017

summary: Comparative analysis of regulation of gene expression by Blimp1 in regulatory and effector CD4+ T cells. The hypothesis tested in the present study was that Blimp1 differentially regualte gene expression in different T cell subsets. Results provide important information of mechanisms underlying regulation of gene expression by Blimp1 in T cells

overall_design: Allotype marked Foxp3GFP reporter Blimp1-sufficient and Blimp1-deficient naïve (CD4+CD44low) T cells were transferred at a 1:1 ratio to RAG1-/- mice. Six-eight weeks later cells were sorted based on Foxp3, CD4 and allotype marker expression, generating 4 different groups (Blimp1 sufficient and Blimp1-defficent regulatory (CD4+Foxp3+) and Blimp1-sufficient and Blimp1-deficient effector (CD4+Foxp3-) T cells

first: Rashmi

last: Bankoti

first: Chihiro

last: Ogawa

first: Jordan

last: Brown

first: Vincent

last: Funari

first: Gislaine

last: Martins


title: DNase-seq during MCF10A-ER-Src cell transformation

status: Public on Jul 03 2017

first: Zhe

last: Ji

summary: We performed DNase-seq to study the dynamic genome-wide chromatin accessibility  during MCF10A-ER-Src cell transformation.

overall_design: DNase-seq at 0, 6, 24 hr during MCF10A-ER-Src cell transformation

first: John

last: Stamatoyannopoulos

first: Kevin

last: Struhl


title: RNA-seq during MCF10A-ER-Src cell transformation and upon factor knockdowns

summary: We performed RNA-seq to examine RNA expression profiles during MCF10A-ER-Src cell transformation and upon knockdowns of transcription factors

overall_design: RNA-seq before and after MCF10A-ER-Src cell transformation, and RNA-seq upon factor knockdowns after inducing cell transformation

first: Lizhi

last: He


title: ChIP-seq for histone modifications during MCF10A-ER-Src cell transformation

summary: We performed ChIP-seq for histone modifications to map chromatin status and dynamics during MCF10A-ER-Src cell transformation.

overall_design: ChIP-seq for H3K27ac, H3K4me3, H3K4me1, H3K36me3, H3K27me3 and H3K9me3 at 0, 2, 12, 24 and 36 hr during MCF10A-ER-Src cell transformation

first: Andreas

last: Janzer

first: Christine

middle: S

last: Cheng

first: Aviv

last: Regev


title: Function and hormonal regulation of GATA3 in human first trimester placentation

status: Public on Jun 13 2017

first: AGCT

last: Core

summary: The transcription factor GATA3 is down regulated by estrogen and plays a role in trophoblast cell function and placentation.

overall_design: To identify downstream genes involved in GATA3 regulation of trophoblast function, we performed RNA sequencing of GATA3 knockdown HTR8/SVneo cells. First, GATA3 expression in HTR8/SVneo cells were knocked down by siRNA transfection and the reduction in GATA3 expression confirmed. Then, gene expression profiles of GATA3 knockdown cells were determined using RNA sequencing on the Illumina NextSeq 500.

first: Bora

last: Lee

first: Lindsay

last: Kroener

first: Ning

last: Xu

first: Erica

last: Wang

first: Alexandra

last: Banks

last: Williams

first: Mark

middle: O

last: Goodarzi

first: Yii-der

middle: I

first: Jie

last: Tang

first: Yizhou

first: Vineela

last: Gangalapudi

first: Margareta

last: Pisarska


title: Single Cell Analysis of Pulmonary Fibrotic Mesenchymal Cells Indicates a New Subtype

status: Public on Mar 29 2018

summary: Stromal  taxonomy consists of multiple cell subtypes that play a critical role in tissue repair or regeneration, fibrosis, inflammation, angiogenesis and tumor formation. However, their identities are not fully understood, as these conventional classified populations have historically been defined by restricted sets of markers. We performed single-cell RNA sequencing to investigate stromal mesenchymal cells (MCs) in normal and fibrotic mouse lung. Interrogated patterns of signature genes, lncRNAs, extracellular and plasma membrane genes, and top transcription factors expression were defined to characterize and classify 7 MC types in normal status. A specific new subset was discovered in fibrotic stage. Delineation of their differentiation trajectory was achieved by a machine learning method. This collection of transcriptional scRNA-seq data uncovered core information and provided a valuable resource for understanding the mesenchymal landscape in fibrotic diseases.

overall_design: Stratification of lung mesenchymal subtypes in normal and fibrotic stages.

first: T

last: Xie

first: Y

first: J

first: P

middle: W

last: Noble

first: D

last: Jiang


title: p53 is a critical regulator of airway epithelial progenitor cell homeostasis.

status: Public on Nov 22 2016

first: AGCT

summary: How progenitor cells regulate quiescence and differentiation is poorly understood. Here, we demonstrate that the tumor suppressor p53 regulates both proliferation and differentiation of club progenitor cells in the airway epithelium. We show that p53 loss decreases ciliated cell differentiation and increases the proliferative capacity of club progenitors, increasing epithelial cell density. p53 deficient progenitors generated a pseudostratified epithelium containing basal-like cells in vitro and contained an increased proportion of BASCs in vivo, suggesting that p53 suppresses multipotency during homeostasis. Conversely, an additional copy of p53 decreases proliferation and increases ciliated cell differentiation. Using single cell RNA-Seq, we expose heterogeneity within airway epithelial progenitor cells and found that cell cycle regulators, particularly p21, are altered following p53 loss. Together, these findings reveal an essential role for p53 in regulating progenitor cell behavior, which has broad implications in understanding both stem cell and cancer biology

overall_design: Examination of progenitor cell behavior in p53 knock out and wild type

first: Alicia

last: Farin

first: Alyson

last: Yeckes

first: Anna

last: Selvagio

first: David

middle: G

last: Kirsch

first: Barry

last: Stripp


title: Extensive translational regulation during seed germination revealed by translational profiling

status: Public on Nov 18 2016

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

summary:
We analysed the translatome and transcriptome of  Arabidopsis thaliana Col-0 WT  at five distinct physiological states during seed germination.
The aim was to obtain a global overview of genes under translational control during seed-seedling transition.

overall_design: Gene expression in dry seeds, 6, 26, 48 and 72 hours after imbibition were performed on both translatome and transcriptome level. The data was used to generate a dynamic map of genes translational relgulated during the transition from seed to seedling with 3 biological replicates for each stage.

first: Bing

last: Bai

first: Alessia

last: Peviani

first: Sjors

last: van der Horst

first: Magdalena

last: Gamm

first: Berend

last: Snel

first: Johannes

last: Hanson


title: NAD+ Analog-sensitive PARPs Reveal a Role for PARP-1 in Transcription Elongation

status: Public on Jun 09 2016

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: The PARP family of proteins comprises 17 members, about two thirds of which are active mono- or poly(ADP-ribosyl)transferase enzymes that transfer the ADP-ribose moiety of NAD+ onto target proteins.  In many cases, ADP-ribosylation, which plays critical roles in human diseases (e.g., cancer, heart disease, and neuropathies) is associated with abrogation of the molecular functions of the target.  Discerning ADP-ribosylation events mediated by a specific PARP is challenging, since all PARPs use the same substrate (i.e., NAD+) and the available inhibitors lack the specificity needed to make such conclusions.  In order to identify the direct and specific targets of individual PARP family members, we have developed a chemical and genetic approach known as analog sensitivity, in which alteration of a single conserved amino acid in the active site of the PARP protein creates a pocket that allows use of an unnatural NAD+ analog containing a steric moiety.  We have functionalized the steric moiety with alkyne for use in click chemistry reactions.  This approach, which is transferable to other PARP family members, creates substrate specificity where none previously existed, allowing PARP-specific post-translational modification followed by target visualization, or isolation of ADP-ribosylated targets using click chemistry techniques.  We have used this technology in conjunction with mass spectrometry to identify hundreds of targets both unique to, as well as shared among, the nuclear PARP proteins, PARP-1, PARP-2, and PARP-3.  We have also determined the genome-wide distribution of PARP-1-specific ADP-ribosylation by coupling this analog-sensitive PARP approach with chromatin cross-linking in method that we call “Click-ChIP-seq”.  We observed that PARP-1-specific ADP-ribosylation is enriched at transcriptionally active promoters in proximity to sites of PARP-1 enrichment.  In addition, we observed that NELF, an important regulator of RNA Polymerase II (Pol II) pausing, is not only a target of ADP-ribosylation by PARP-1 but also spatially correlated with chromatin-associated ADP-ribose and PARP-1 in Click-ChIP-seq and ChIP-seq assays, respectively.  Given these observations, we hypothesized that ADP-ribosylation might modulate NELF function and result altered Pol II pausing.  We have explored this possibility using global run-on coupled with deep sequencing (GRO-seq) in MCF-7 cells in which PARP-1 was depleted by RNAi-mediated knockdown.  PARP-1 depletion caused an increase in Pol II pausing genome-wide.  Taken together, these results suggest the intriguing possibility that ADP-ribosylation of NELF by PARP-1 may be an important and heretofore unknown step in the release of Pol II into productive elongation.

overall_design:
Using GRO-seq (knockdown of Luciferase [control] with or without PARP inhibitor [PJ34] treatment and knockdown of PARP-1) and RNA-seq (knockdown of Luciferase [control] with or without CDK inhibitor [DRB] treatment and knockdown of PARP-1)  in MCF-7 human breast cancer cells.
Using GRO-seq upon 17b-estradiol (E2) treatment in MCF-7 cells.

first: Bryan

last: Gibson

first: Kristine

last: Frizzell

first: Minho

last: Chae

first: W


title: HOX13 activity reprograms cis-regulatory modules during digit development (RNA-Seq)

status: Public on Dec 14 2016

city: montreal

first: Rushikesh

last: Sheth

address: 110 avenue des pins ouest

department: Genetics and Development

country: Canada

institute: IRCM

summary: The combinatorial expression of the Hox genes along the body axes, referred to as the HOX code, is a major determinant of cell fate and plays a prevailing role in generating the animal body plan. In developing limb buds, the paralogous group 13 genes of the HoxA and HoxD clusters are essential for patterning the distal-most limb structures, the digits. Inactivation of HOXA13 and HOXD13 transcription factors (HOX13) leads to complete digit agenesis in mice, but how HOX13 regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here we performed genome-wide profiling of HOX13 by chromatin immunoprecipitation and analyzed the transcriptome and chromatin state of wild type early and late-distal limb buds, as well as Hoxa13-/-;Hoxd13-/- compound mutant limb buds. Our results show that inactivation of HOX13 impairs the activation and repression of putative cis-regulatory modules specific to the late-distal limb cells. Loss of HOX13 also disrupts the specific, spatial patterning of gene expression along the proximal-distal axis of the developing limb buds. These results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.

overall_design: Totla mRNAs from dissected distal parts of e11.5 forelimb, of wild-type as well as Hoxa13-/-;Hoxd13-/- mice

first: Iros

last: Barozzi

last: Langlais

first: Marco

last: Osterwalder

first: Stephen

last: Nemec

first: H

last: Stadler

first: Axel

last: Visel

first: Jacques

last: Drouin

first: Marie

last: Kmita


title: DNaseI hypersensitivity assay and ER, GR, and FoxA1 binding patterns in breast cancer cells

status: Public on Apr 08 2016

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Comprehensive transcriptome profiling reveals multigene signatures in triple negative breast cancer

status: Public on Jan 04 2016

city: Shanghai

first: Yi-Zhou

last: Jiang

state: Shanghai

address: No. 270 Dong-An Road

institute: Fudan University Shanghai Cancer Center

summary: To develop and validate novel multigene signatures to facilitate individualized treatment of TNBC patients By integrating expression profiles of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs).

overall_design: We analysed 165 TNBC samples and 33 paired normal breast tissues using transcriptome microarrays. Tumor-specific mRNAs and lncRNAs were identified and correlated with patients’ recurrence-free survival (RFS). Using Cox regression model, we built two multigene signatures incorporating mRNAs and lncRNAs. The prognostic and predictive accuracy of the signatures were tested in a training set of 165 TNBC patients and validated in another 101 TNBC patients.

first: Yi-Rong

last: Liu

first: Xiao-En

last: Xu

first: Xin

last: Hu

first: Ke-Da

last: Yu

first: Zhi-Ming

last: Shao


title: Dissecting the heterogeneity of skin gene expression patterns in systemic sclerosis.

status: Public on May 26 2015

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: We identified fibro-inflammatory and keratin gene expression signatures in systemic sclerosis skin.

overall_design: Skin biopsy samples from 61 patients enrolled in the GENISOS cohort or an open label imatinib study (baseline sample) and 36 controls were examined by global gene expression studies.  5 patients were sampled at two time points (early-late).  There is overlap between this data set and GSE47162.

first: Shervin

last: Assassi

first: William

last: Swindell

first: Minghua

last: Wu

first: Filemon

last: Tan

first: Dinesh

last: Khanna

first: Daniel

middle: E

last: Furst

first: Donald

last: Tashkin

first: Richard

last: Jahan-Tigh

first: Maureen

last: Mayes

first: Johann

last: Gudjonsson

middle: T


title: Transcriptomic study of biological networks involving grapevine berry development

status: Public on Jan 27 2016

city: Nanjing

first: Lingfei

last: Shangguan

state: Jiangsu

address: 1 Weigang Rd

department: Horticultural Department

institute: Nanjing Agri. University

summary: De-multiplexing the unique identifiers discovered data consisted of 28,808,716 clean reads from fruit samples at 40 DAF, 27,941,132 reads from 65 DAF, and 25,457,565 reads from fruit sample at 90 DAF.

overall_design: To discover the whole transcriptomic change during grapevine fruit development (Sample number: 3, Sequencing platform: Illumina HiseqTM2500

first: Jinggui

last: Fang


title: ChIP-seq of MSL1 in male and female fly samples

status: Public on Apr 25 2016

city: New York

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

summary: We report the binding of MSL1 protein in  male, female and mof2 mutant samples of Drosophila melanogaster and Drosophila virilis

sample_organism:
Drosophila melanogaster
Drosophila virilis

first: Thomas

last: Conrad

first: Sarantis

last: Chlamydas

first: Sunil

middle: J

last: Raja

first: Fidel

last: Ramirez

first: Filipe

last: Cadete

first: Asifa

last: Akhtar


title: A nested case-control study to investigate drivers for metastatic disease in breast cancer

status: Public on Jul 08 2015

city: Stockholm

first: Alexandra

last: Jauhiainen

address: PO Box 281

department: Medical Epidemiology and Biostatistics

institute: Karolinska Institutet

summary:
The purpose of this study was to improve prediction of patients at high-risk for metastatic disease utilizing a nested case-control design that uniquely enables enrichment for relevant phenotypes. We identified all women diagnosed with primary breast cancer from January 1, 1997, to December 31, 2005, in the Stockholm health care region. Patients developing distant metastatic disease (cases) were selected and controls (free from distant disease) were randomly matched by adjuvant therapy, age and calendar period at diagnosis. The nested case-control study included 768 study subjects with clinical information and gene expression arrays (Human Cancer G110).
Study subjects were randomly and equally divided into training set (discovery) or testing (validation) set. Metastatic onset prediction was then compared including either clinical variables only or combining clinical and genetic information. Differentially expressed genes and pathways between cases and controls included a wide-spectrum of well known as well as candidate regulators of the metastatic cascade.

overall_design: The nested case-control study included 768 study subjects corresponding to 623 primary tumor samples. Details concerning case-control status are given in the samples section. Each case and its' matching controls form risk sets, indicated by the setnr variable.

first: Linda

last: Lindström

first: Kamila

last: Czene

first: Jonas

last: Bergh


title: Chemopreventive effect of flaxseed-enriched diet on ovarian cancer in laying hen.

status: Public on May 18 2015

city: Carbondale

first: Dale

middle: Buchanan

last: Hales

address: 1125 Lincoln Drive,Life Science II, Room 245 (M/C 6512), Southern Illinois University

department: Physiology

institute: School of Medicine, Southern Illinois University

summary: The objective of this study was to identify the molecular mechanisms and biological pathways associated with the anticancer effects of flaxseed (richest plant source of Omega-3 fatty acid) in laying hen model of ovarian cancer.  Study shows a significant reduction in the severity of the disease and increased survival of the laying hens fed with flaxseed.

overall_design: 2 X 2 condition experiment, Diet (Control & Flaxseed fed) and Tissue (Normal & Cancer). Biological replicates: 6 control normal replicates, 6 control cancer replicates, 6 flaxseed normal replicates and 6 flaxseed cancer replicates.

first: Nawneet

middle: K

last: Kurrey

first: Karen

middle: H

first: Yan

last: Zhuge


title: Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation

city: Chicago

first: Zhe

last: Ji

institute: Northwestern University


title: Effects of miR-125b expression on the transcriptome of B cell precursors

status: Public on Jan 01 2015

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

institute: Medical University of Innsbruck, Biocenter

summary: Here, we have screened a miRNA expression library in a pre-B cell expression system to identify miRNAs with a potential oncogenic activity in early lymphocytes. We show that miR-125b is sufficient to transform B cell precursors in vitro as defined by growth factor independence, and demonstrate that continuous expression of miR-125b is necessary to keep cells in the transformed cells. Mechanistically, we find that expression of miR-125b protects against apoptosis induced by growth factor withdrawal, and that miR-125 interferes with the differentiation of pre-B to immature B cells. In consequence, transformed cells express the pre-BCR on the cell surface, which appears to provide signals for ongoing proliferation and survival. Using microarray analysis, we identified several previously known and novel putative target genes of miR-125b in B cell precursors. To evaluate their contribution to the miR-125b-mediated phenotype, transformed cells were reconstituted with expression constructs of validated target genes. Surprisingly, we only find that reconstitution of MAP3K11 interferes with the cellular fitness of transformed cells in vitro as well as in vivo. This indicates that MAP3K11 functions as an important tumor suppressor in the context of miR-125b.

overall_design: Gene expression in cells expressing a control vector or a vector encoding hsa-miR-125b-1 was measured either in the presence or 24 hours after withdrawal of the growth factor IL-7. Two independent experiments were performed, using independently generated cell clones for each repetition.


title: Characterization of ER, GR, and FoxA1 binding patterns in breast cancer cells treated with either Dex or E2

first: Songjoon

last: Baek

summary: The estrogen receptor (ER), glucocorticoid receptor (GR), and forkhead box protein 1 (FoxA1) are significant factors in breast cancer progression.  FoxA1 is well-established as a pioneer factor for steroid receptor recruitment to chromatin.  Here we show that ER and GR have the ability to alter the genomic response of FoxA1 to specific binding sites within the genome.  These findings alter the classical understood mechanism of FoxA1 establishing a dynamic transcription factor that can be regulated by hormones.

overall_design: We examined the ER and GR mediated affects on FoxA1 binding patterms

first: Erin

last: Swinstead

first: Gordon

middle: L

last: Hager


title: The developmental dynamics and disease potential of random monoallelic gene expression

status: Public on Feb 27 2014

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: X-chromosome inactivation (XCI) in females and allelic exclusion of olfactory receptor or immunoglobulin loci, represent classic examples of random monoallelic expression (RME). RME of some single copy genes has also been reported, but the in vivo relevance of this remains unclear. Here we identify several hundred RME genes in clonal neural progenitor cell lines derived from embryonic stem cells. RME occurs during differentiation and once established, the monoallelic state can be highly stable. We show that monoallelic expression also occurs in vivo, in the absence of DNA sequence polymorphism, similarly to XCI. Several of the genes identified play important roles in development and have also been implicated in human autosomal dominant disorders. We propose that monoallelic expression of such genes contributes to the fine-tuning of the developmental regulatory pathways they control and in the context of a mutation, RME can predispose to loss of function in a proportion of cells and thus contribute to disease.

overall_design: The hybrid mouse ES cell lines F1-21.6 and F1-23 (129Sv-Cast/EiJ), previously described in (Luikenhuis et al., 2001) and (Jonkers et al., 2009), were grown on mitomycin C-inactivated MEFs in ES cell media containing 15% FBS (Gibco), 10-4 M b-mercaptoethanol (Sigma), 1000U/ml of leukaemia inhibitory factor (LIF, Chemicon). Mouse ES cells were differentiated into neural progenitor cells (NPC) as previously described (Conti et al., 2005; Splinter et al., 2011). Total RNAs were prepared from the mouse ES cell lines, 4 NPC clones derived from ES cell line F1-21.6 plus one replicate, and 4 NPC clones derived from ES cell line F1-23 plus one replicate. Library preparation after polyadenylated RNA purification was performed according to the standard Illumina instructions. Paired-end 100bp reads were generated using the HiSeq 2000 sequencing platform.

first: Anne-Valerie

last: Gendrel

first: Mikael

last: Attia

first: Chong-Jian

last: Chen

first: Patricia

last: Diabangouaya

first: Emmanuel

last: Barillot

first: Edith

last: Heard


title: Gene expression in rectal epithelia of cystic fibrosis patients

status: Public on Nov 28 2013

city: Heidelberg

first: Stefan

last: Wolfl

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

institute: Heidelberg University, Heidelberg, Germany

summary: Gene expression profiles were recorded from rectal suction specimens of Cystic Fibrosis (CF) patients, carrying the CF-specific D508 mutated CFTR-allele.  These profiles were compared with gene expression profiles from rectal suction specimens of non-CF subjects (control).

overall_design:
We used Affymetrix GeneChip HG-U133A microarrays to record the gene expression profile of 16 CF and 13 non-CF individuals.
Rectal suction specimens representing rectal mucosal epithelia were collected from CF patients and non-CF individuals. Biopsies were analyzed for residual function using ICM and total RNA was isolation immediately using the Qiagen RNeasy protocol with on column DNA digestion.  About 1-5 µg RNA were obtained from each individual. Integrity of total RNA samples was monitored by gel-electrophoresis before cDNA synthesis. Labeled cRNA synthesis and hybridization was performed following standard protocols.

last: Wölfl

first: Larissa

last: Pusch

first: Torsten

middle: C

last: Kroll

first: Andrea

last: van Barneveld

first: Frauke

last: Stanke

first: Stefanie

last: Tamm

first: Benny

last: Siebert

first: Manfred

last: Ballmann

first: Sybille

last: Junge

first: Burkhard

last: Tümmler


title: Global hepatic transcript data from fasted male BXD strains on chow or high fat diet

status: Public on Sep 11 2014

city: Lausanne

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

institute: École Polytechnique Fédérale de Lausanne

summary:
Transcript data from livers from fasted-state BXD strains on chow or high fat diet
We used microarrays to compare the hepatic expression differences across the BXD strain family and across two diverse diets

overall_design: 29-week-old male mice were fasted overnight (6pm-9am), anesthetized under isoflurane, and perfused, then livers were snap-frozen in liquid nitrogen for RNA extraction and RNEasy cleanup. Each dietary and strain cohort consisted of ~5 animals which were prepared independently then pooled evenly by µg RNA before the Affymetrix arrays were run.

first: Evan

last: Williams


title: Effects of miRNA sponge/decoy-mediated reduction of miR-15 family activity on the transcriptome of B cell precursors

status: Public on Jan 01 2016

first: Sebastian

last: Herzog

summary:
A common experimental setup to investigate the function of a microRNA is a “gain-of-function” approach, in which the microRNA of interest is overexpressed to analyze its impact on a given process. However, a major drawback of this technique is that microRNAs, when expressed significantly above endogenous levels, may target genes that are not affected under physiological conditions. To circumvent this problem, we have generated a retroviral microRNA-knockdown library encompassing the majority of the microRNA families expressed throughout lymphocyte development. MicroRNA knockdown is mediated by sponges, mRNAs that possess multiple binding sites for a certain microRNA family in their 3’-UTR region. MiRNA sponges function as competitive inhibitors that sequester all specific microRNA/RISC complexes, thereby de-repressing the endogenous target genes.
Using this library in pre-B cells as a model system, we have characterized all microRNAs expressed in early B cells development according to their impact on processes such as apoptosis and differentiation. In doing so, we show that functional knockdown of the known tumor-suppressive miR-15 family has only slight effects under cellular steady-state conditions. Upon withdrawal of the growth factor IL-7, however, loss of miR-15 function almost completely inhibits pre-B to immature B cell differentiation, partially protects from apoptosis and enables prolonged proliferation. In correspondence with that, knockdown of the miR-15 family confers a competitive advantage in suboptimal IL-7 concentrations, indicating that levels of miR-15 determine the sensitivity of cells towards growth factor receptor signaling. Moreover, IL-7 withdrawal seems to increase the activity of endogenous miR-15 family members in pre-B cells.
Using microarray analysis, we have identified cyclin E1 as a direct and cyclin D3 as an indirect putative target gene of the miR-15 family in B cell precursors. Exogenous expression of cyclin E1 or cyclin D3 recapitulates the miR-15 loss-of-function phenotype in B cell precursors, validating their biological importance.
Together, this suggests that the miR-15 family functions as a central element in a positive feedback loop that reinforces cell-cycle arrest at low growth factor concentrations, which is considered a prerequisite for light chain gene recombination and differentiation.

overall_design: Gene expression in cells expressing a scrambled sponge as a control vector or a sponge designed to sequester all members of the miR-15 family (miR-15a, miR-15b, miR-16, miR-497, miR-195, miR-322) was measured either in the presence or 36 hours after withdrawal of the growth factor IL-7. Two independent experiments were performed, using independently generated cell clones for each repetition.


title: Expression Signatures Identify Origin of Primary and Therapeutic Strategies for Patients with Advanced Solid Tumors

status: Public on Feb 13 2016

city: Durham

first: David

last: Hsu

state: NC

address: Rm 2167 CIEMAS Bldg, 101 Science Dr.

department: Institute for Genome Sciences and Policy

institute: Duke University

summary:
Background: Fatal cancer is often the result of spread, or metastasis, of a cancer cell from the site of its origin to a distant anatomic site. While the metastatic process and the foreign environment of the metastatic site impact a tumor’s biology, we continue to determine therapy for patients based upon their cancer’s site of origin. We have performed an unbiased analysis across metastatic solid tumors from common primary sites to determine the molecular impact of the metastatic process on site-specific biology and to identify novel therapeutic strategies.
Methods: Global gene expression was used as a biological phenotype to perform a top-down analysis of 96 metastatic human tumors. Laser capture microdissection, RNA amplification, and microarray analysis were used to measure the transcription patterns of malignant epithelial cells.  Genes, multi-gene expression “signatures”, and pathways associated with site of origin (SOO) and site of metastases (SOM) were identified using established computational approaches. SOO and SOM expression signatures were validated on multiple, independent datasets comprising 1217 samples (1104 samples from GSE2109 (Expression Project for Oncology) and 113 samples from GSE12630 (Monzon FA, Lyons-Weiler M, Buturovic LJ, Rigl CT et al. Multicenter validation of a 1,550-gene expression profile for identification of tumor tissue of origin. J Clin Oncol 2009 May 20;27(15):2503-8. PMID: 19332734). Reverse phase proteomics and in vitro tissue culture were used to validate associations between biological pathways, site of primary, and implicated therapeutic combinations.
Findings: SOO has the dominant influence on solid tumor biology as samples segregate based upon their primary site during unsupervised hierarchical clustering. In addition, statistically significant associations are identified between single genes and pathways and each primary site investigated and SOO signatures for colon, breast, ovary, lung, and prostate cancers accurately identify primary site for independent samples of both local and metastatic tumors independent of degree of histological differentiation. The impact of SOM on tumor biology is evident as genes and pathways are significantly associated with metastatic site and SOM signatures can be generated but they are not strongly predictive when applied to localized tumors. Pathway analysis identified relatively increased expression of MYC, beta-catenin, and SRC gene sets in metastatic colorectal cancers which was confirmed with proteomic analysis of a sub-set of the original tumors. Within colorectal cancers, high SRC expression also correlates with predicted oxaliplatin sensitivity and the combination of an SRC inhibitor with oxaliplatin demonstrated synergy in three independent colorectal cancer cell lines.
Interpretation: Our findings suggest that the complex alterations required for metastasis do not obscure the impact of a cancer cell’s origin. SOO signatures have the potential to be highly accurate diagnostic tools and the underlying site-specific biology can be used to identify novel therapeutic targets for advanced cancers.

Keywords: Gene expression analysis

overall_design:
Ninety-six laser capture microdissected adenocarcinoma patient tumor samples of various primary and metastatic sites were processed for Total RNA. Our 96-sample datatset was enriched by inclusion of previously deposited microarray data in GEO (reprocessed for this study):
A total of 1217 samples (1104 samples from GSE2109, 113 samples from GSE12630) were reprocessed from the CEL files using RMA.
Supplementary files:
The reprocessed data matrices.
A list of the 1217 Samples' GSM accession numbers and the corresponding reprocessed sample IDs.

first: Mickey

last: Kim

first: Adam

last: Foye

first: Alessandra

last: Silvestri

first: Bala

last: Balakumaran

first: Herbert

last: Lyerly

first: Michael

middle: A

last: Morse

first: Emanuel

last: Petricoin

first: Phillip

last: Febbo


title: Comparative Gene Expression Profiling Analysis of Urothelial Carcinoma of Renal Pelvis and Bladder

status: Public on Dec 31 2010

city: Grand Rapids

first: Bin

middle: Tean

last: Teh

state: MI

address: 330 Bostwick Av

department: Cancer Genetics

institute: Van Andel Institute

summary:
Expression profiling by arrays
Urothelial carcinoma (UC) can arise at any location along the urothelial tract, including the urethra, bladder, ureter or renal pelvis. Although tumors arising in these various locations demonstrate similar morphology, it is unclear whether the gene expression profiles are similar in the upper tract (ureter and renal pelvis) or in the lower tract (bladder and urethra) carcinomas, especially given their different embryologic origins. As differences may facilitate potentially different screening and treatment modalities, we sought to examine the relationship between urothelial carcinoma of the renal pelvis (rUC) and urothelial carcinoma of the bladder (bUC). Fresh tumor tissue was collected from patients with bUC (n=10) and benign mucosa from the bladder (n=7) was collected from individuals undergoing resection for non-UC conditions for comparison. Gene expression profiles from these samples were determined using high-throughput Affymetrix gene expression microarray chips. Bioinformatic approaches were used to compare gene expression profiles of these samples and those of rUC (n= 14) and normal kidney (n=14) that were mostly used in our previous publication.  Using unsupervised analytic approaches, rUC and bUC were indistinguishable. When supervised analytic approach was used, a very small number of potentially differentially expressed genes was identified; these differences were most likely to be limited to a single pathway - the chloride ion binding activity pathway -which was more frequently activated in rUC than in bUC. We found that the gene expression profiles of UCs from the upper and lower tract were extremely similar, suggesting that similar pathogenic mechanisms likely function in the development of these tumors. The differential expression of genes in the identified pathway may represent a potential new avenue for detection of upper tract tumors.

overall_design: Tissue samples with urothelial cell carcinoma from   lower tract (bladder)  as well as normal references  were collected and the gene expression profiles were compared with gene expression profiles of samples in our previously published data set . No technical replicates.

first: Donna

last: Hansel

first: Zhongfa

last: Zhang


title: Novel long non-coding RNAs are involved in cellular response to angiotensin II signaling

status: Public on Jun 30 2013

city: Duarte

first: Amy

last: Leung

address: 1500 E. Duarte Rd

department: Diabetes/Cancer

institute: Beckman Research Institute, City of Hope

summary: Angiotensin II (AngII) is a polypeptide hormone that plays a pivotal role in the regulation of blood pressure. In vascular smooth muscle cells (VSMCs), AngII signaling results in hypertrophy, proliferation, contraction, and migration, which ultimately promote atherosclerosis and hypertensive cardiovascular diseases. Recent studies have shown that fundamental biological processes such as cell proliferation and differentiation are mediated in part by the activities of long non-protein-coding RNAs (lncRNAs). In this study, we sought to identify lncRNAs that are involved in the response to AngII-signaling. Genome-wide analysis of de novo assembled transcripts from rat vascular smooth muscle cells (VSMCs) identified novel lncRNA as well as protein-coding transcripts which have not been previously annotated. The majority of the genomic loci from which these novel transcripts are transcribed are enriched for histone H3 lysine 4 trimethylation and histone H3 lysine 36 trimethylation, two chromatin modifications that are closely associated with actively transcribed regions, further supporting these as bona fide transcripts. Compared with previously annotated rat transcripts, these novel lncRNA transcripts, on average, are shorter in length and are less abundant, consistent with reports from mice and humans. Expression analyses of transcripts from control and AngII-stimulated VSMCs reveal that AngII signaling affects the abundance of both protein-coding transcripts as well as lncRNAs transcripts. Altogether, these data provide new insights into the global effects of AngII signaling and reveal potential novel therapeutic targets for treatment of AngII-associated cardiovascular diseases.

overall_design: RNA-sequencing of control and AngII (3hrs)-stimulated rVSMSCs. ChIP-sequencing of H3K4me3 and H3K36me3 in control and AngII (3hrs)-stimulated rVSMCs.

first: Dustin

last: Schones

first: Rama

middle: N

last: Natarajan

first: Linda

last: Lanting

first: Candi

last: Trac


title: Transcript analysis in response to ozone in mice deficient in TLR4

status: Public on Feb 29 2012

city: Aurora

first: Alison

middle: Kendall

last: Bauer

state: CO

address: 12850 E. Montview Blvd.; Rm 3125

department: Environmental and Occupational Health

institute: University of Colorado Denver

summary: We previously identified toll-like receptor 4 (Tlr4) as a candidate gene responsible for ozone (O3)-induced pulmonary hyperpermeability and inflammation. The objective of this study was to determine the mechanism through which TLR4 modulates O3-induced pulmonary responses and to utilize transcriptomics to determine TLR4 effector molecules. C3H/HeJ (HeJ; Tlr4 mutant) and C3H/HeOuJ (OuJ; Tlr4 normal), mice were exposed continuously to 0.3 ppm O3 or filtered air for 6, 24, 48 or 72 hr. Affymetrix Mouse430A_MOE gene arrays were used to analyze lung homogenates from HeJ and OuJ mice followed using a bioinformatic analysis. Inflammation was assessed by bronchoalveolar lavage and molecular analysis by ELISA, immunoblotting, and transcription factor activity. TLR4 signals through both the MYD88-dependent and independent pathways in OuJ mice, which involves MAP kinase activation, NF-kappaB, AP-1, and KC. Microarray analyses identifiedTLR4 responsive genes for strain and time in OuJ versus HeJ mice (p<0.05). One significantly upregulated cluster of genes in OuJ were the heat shock proteins (Hspa1b; Hsp70), Hsp90ab1). Furthermore, O3-induced expression of HSP70 protein was increased in OuJ compared to HeJ mice following 24-48 h O3. Moreover, BAL polymorphonuclear leukocytes (PMN) and total protein were significantly reduced in response to O3 in Hspa1a/Hspa1btm1Dix (Hsp70-/-) compared to Hsp70+/+ mice (p<0.05). TLR4 signaling (MYD88-dependent), ERK1/2, AP-1 activity, and KC protein content were also significantly reduced after O3 exposure in Hsp70-/- compared to Hsp70+/+ mice (p<0.05). These studies suggest that HSP70 is involved in the regulation of O3-induced lung inflammation through the TLR4 pathway and provide evidence that HSP70 is an endogenous in vivo TLR4 ligand.

overall_design: Two strains of mice were used for these studies. The C3H/HeJ with a dominant negative Tlr4 and the C3H/HeOuJ mice with a sufficient Tlr4. Total RNA was extracted from left lung lobes (air, 6, 24, 48 hr of O3 exposure for OuJ and HeJ mice; n = 3 per treatment group).  Therefore a total of 24 arrays with 3 different ozone exposure times and 1 air exposure.

first: Elizabeth

last: Rondini

first: Kristin

last: Hummel

first: Laura

middle: M

last: Degraff

first: Christopher

last: Walker

first: Anne

last: Jedlicka

first: Steven

middle: R

last: Kleeberger


title: An Integrated Approach to Understanding Host-Pathogen Interactions

status: Public on Jan 30 2017

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

summary: This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE58340
SuperSeries of: GSE94273
SuperSeries of: GSE99486
SuperSeries of: GSE103042
SuperSeries of: GSE103259
SuperSeries of: GSE103507
SuperSeries of: GSE104101
SuperSeries of: GSE104223
SuperSeries of: GSE104330
SuperSeries of: GSE110970
SuperSeries of: GSE123495
SuperSeries of: GSE127079
SuperSeries of: GSE128115

sample_organism:
Plasmodium knowlesi
Macaca fascicularis
Macaca mulatta
Plasmodium coatneyi
Plasmodium cynomolgi strain B
Plasmodium cynomolgi ceylonensis


title: Model of heart failure induced by mild thiol-blocking with cystamine

status: Public on Dec 03 2010

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

institute: ETH Zurich

summary: Depletion of cardiac ATP content is a characteristic feature of heart failure in patients and experimental animal models. To analyze the impact of insufficient ATP supply on heart function we inhibited cellular respiration by disulfide poisoning with the mild thiol-blocking agent, cystamine. We chose 4 month-old apolipoprotein E (apoE)-deficient mice, which are highly vulnerable to increased oxygen and ATP demands. After 4 weeks of cystamine treatment (300 mg/kg in drinking water), echocardiography and histology analyses demonstrated that apoE-deficient mice had developed heart failure with cardiac dilation. The microarray gene expression study of heart tissue from cystamine-treated apoE-deficient mice relative to untreated mice confirmed the development of heart failure showing up-regulation heart failure-specific genes by mild thiol-blocking with cystamine.

overall_design: Microarray gene expression profiling was performed with heart tissue isolated from three study groups: (i) cystamine-treated 5 month-old apolipoprotein- (apoE)- deficient mice with symptoms of heart failure, (ii) untreated 5 month-old apoE- deficient mice, and (iii) age-matched, untreated, non-transgenic B6 control mice.

first: Said

last: AbdAlla


title: Microarray gene expression profiling of cardiac genes at the onset of heart failure

summary: Atherosclerosis and pressure overload are major risk factors for the development of heart failure in patients. Cardiac hypertrophy often precedes the development of heart failure. However, underlying mechanisms are incompletely understood. To investigate pathomechanisms underlying the transition from cardiac hypertrophy to heart failure we used experimental models of atherosclerosis- and pressure overload-induced cardiac hypertrophy and failure, i.e. apolipoprotein E (apoE)-deficient mice, which develop heart failure at an age of 18 months, and non-transgenic C57BL/6J (B6) mice with heart failure triggered by 6 months of pressure overload induced by abdominal aortic constriction (AAC). The development of heart failure was monitored by echocardiography, invasive hemodynamics and histology. The microarray gene expression study of cardiac genes was performed with heart tissue from failing hearts relative to hypertrophic and healthy heart tissue, respectively. The microarray study revealed that the onset of heart failure was accompanied by a strong up-regulation of cardiac lipid metabolism genes involved in fat synthesis, storage and oxidation.

overall_design: Microarray gene expression profiling was performed with heart tissue isolated from (i) 18 month-old apoE-deficient mice relative to age-matched non-transgenic C57BL/6J (B6) mice, (ii) 6 month-old apoE-deficient mice with 2 months of chronic pressure overload induced by abdominal aortic constriction (AAC) relative to sham-operated apoE-deficient mice and nontransgenic B6 mice, (iii) 10 month-old B6 mice with 6 months of AAC relative to sham-operated B6 mice, and (iv) 5 month-old B6 mice with 1 month of AAC relative to age-matched B6 mice.


title: Cardiac gene expression profiling of apoE-deficient mice receiving heart failure treatment with the anti-ischemic drug ranolazine

summary: Heart failure is a leading cause of cardiovascular mortality with limited options for treatment. We used 18 month-old apolipoprotein E (apoE)- deficient mice as a model of atherosclerosis-induced heart failure to analyze whether the anti-ischemic drug ranolazine could retard the progression of heart failure. The study showed that 2 months of ranolazine treatment improved cardiac function of 18 month-old apoE-deficient mice with symptoms of heart failure as assessed by echocardiography. To identify changes in cardiac gene expression induced by treatment with ranolazine a microarray study was performed with heart tissue from failing hearts relative to ranolazine-treated and healthy control hearts. The microarray approach identified heart failure-specific genes that were normalized during treatment with the anti-ischemic drug ranolazine.

overall_design: Microarray gene expression profiling was performed with heart tissue isolated from (i) untreated 18 month-old apoE-deficient mice with heart failure relative to (ii) 18 month-old apoE-deficient mice treated for two months with the anti-ischemic drug ranolazine (200 mg/kg), and (iii) age-matched non-transgenic C57BL/6J (B6) control mice.


title: Expression data from Myc/Bcl2-transformed primary mouse leukemia cells

status: Public on Sep 01 2016

city: Münster

first: Frank

last: Rosenbauer

address: Robert-Koch-Str. 43

department: Institute of Molecular Tumor Biology

institute: University Hospital Münster

summary: Unfavorable patient survival coincides with the lineage plasticity observed in ~20% of human acute leukemias. These cases are assumed to arise from hematopoietic stem cells, which have stable multipotent differentiation potential. However, here we report that plasticity in leukemia can result from instable lineage identity states inherited from differentiating progenitor cells. Using mice with enhanced c-Myc/Bcl2-expression, we show that T-lymphoid progenitors retain broad malignant lineage switching potential with a high capacity to differentiate into myeloid leukemia.

overall_design: Affymetrix whole genome cDNA expression array data were generated from flow-sorted myeloid (CD11b+Gr1+/CD3–CD4–CD8–) splenocytes of leukemic recipient mice that had received Myc/Bcl2-transformed granulocyte-macrophage-progenitors (GMPs), Lineage-Sca1+c-kit+ (LSK, as a population enriched for hematopoietic stem cells) from the bone marrow or CD4/CD8 double negative 2 (DN2) cells from the thymus of C57/Bl6 CD45.2 donor wildtype mice.

first: Pia

last: Riemke

first: Carolin

last: Walter

first: Martin

last: Dugas


title: Multiple Origins of Virus Persistence during Natural Control of HIV Infection

status: Public on Jul 01 2016

city: BETHESDA

first: Jianfei

last: Hu

address: 40 CONVENT DR

department: Vaccine Research Center

institute: NIH

summary: Targeted HIV cure strategies require definition of the mechanisms that maintain the virus. Here, we tracked HIV replication and the persistence of infected CD4 T cells in individuals with natural virologic control by sequencing viruses, T cell receptor genes, HIV integration sites and cellular transcriptomes. Our results revealed three mechanisms of HIV persistence operating within distinct anatomic and functional compartments. In lymph node, we detected viruses with genetic and transcriptional attributes of active replication in both T follicular helper (TFH) cells and non-TFH memory cells. In blood, we detected inducible proviruses of archival origin among highly differentiated, clonally expanded cells. Linking the lymph node and blood was a small population of circulating cells harboring inducible proviruses of recent origin. Thus, HIV replication in lymphoid tissue, clonal expansion of infected cells, and recirculation of recently infected cells act together to maintain the virus in HIV controllers despite effective antiviral immunity.

overall_design:
Fluorescence-activated cell sorting (FACS) was used to sort subsets of CD4 T cells from blood (peripheral blood mononuclear cells; PBMC) and lymph node from a cohort of HIV-infected people with natural control of the virus (termed HIV controllers). Subsets of CD4 T cells that were sorted are as follows:  from blood, (1) naïve (N), (2) central memory (CM), (3) transitional memory (TM), and (4) effector memory (EM); from lymph node, (1) naïve (N), (2) non-germinal center T-follicular helpers (nGC), (3) germinal center T-follicular helpers (Tfh), (4) effector memory (EM), and (5) other central memory-like subsets (CMPD1lo57lo, CMPD1lo57hi, and/or CMPD1lo).  Total RNA and total DNA were extracted from these sorted subsets in separate fractions using RNAzol RT and DNAzol.  Total cellular DNA was used for HIV quantification and sequence analysis as describe in the publication. Total RNA used for mRNA library construction by oligo-dT purification (Dynabeads), random fragmentation by heating in the presence of Magnesium (in form of 5x first-strand buffer, LifeTech), reverse transcription (SuperScript III), and then second-strand synthesis, end repair, a-tailing, and adaptor ligation using NEBNext enzyme master mixes and oligonucleotides.  Libraries were sequenced on an Illumina HiSeq2000.
Please note that each 'source name' value represent individual who havs HIV infection with natural control of the virus.

first: Daniel

last: Douek

first: Eli

last: Boritz


title: Inhibition of histone deacetylase activity interferes with innate immune responses and protects from severe sepsis

status: Public on Jan 01 2011

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary: Regulated by histone acetyltransferases and deacetylases (HDACs), histone acetylation is a key epigenetic mechanism controlling chromatin structure, DNA accessibility, and gene expression. HDAC inhibitors induce growth arrest, differentiation, and apoptosis of tumor cells and are used as anticancer agents. Here we describe the effects of HDAC inhibitors on microbial sensing by macrophages and dendritic cells in vitro and host defenses against infection in vivo. HDAC inhibitors down-regulated the expression of numerous host defense genes, including pattern recognition receptors, kinases, transcription regulators, cytokines, chemokines, growth factors, and costimulatory molecules as assessed by genome-wide microarray analyses or innate immune responses of macrophages and dendritic cells stimulated with Toll-like receptor agonists. HDAC inhibitors induced the expression of Mi-2β and enhanced the DNA-binding activity of the Mi-2/NuRD complex that acts as a transcriptional repressor of macrophage cytokine production. In vivo, HDAC inhibitors increased the susceptibility to bacterial and fungal infections but conferred protection against toxic and septic shock. Thus, these data identify an essential role for HDAC inhibitors in the regulation of the expression of innate immune genes and host defenses against microbial pathogens.

overall_design: Mus musculus cells were grown in presence of LPS or LPS + TSA and pam or pam + TSA and hybrydised against a cRNA pool UMRR (from Mus musculus cells).

first: Marlies

last: Reymond


title: Comparative gene expression in the human limbus, conjunctiva and cornea

status: Public on Jan 01 2013

city: Los Angeles

last: Nakatsu

address: 200 Stein Plaza

institute: Jules Stein Eye Institute

summary: To date, there is no specific marker for limbal epithelial stem cells. The identification of a marker that is expressed in the limbal epithelium but not in the cornea or conjunctiva epithelium has been a growing need. To search for limbal-specific marker(s), we performed preferential gene profiling in the limbus in direct comparison to that in the cornea and conjunctiva using microarray technique.

overall_design: This study consisted of gene expression profiles comparing the limbus to the  cornea and conjunctiva.

first: Sophie

middle: X

last: Deng


title: Cardiac gene expression profiling of heart failure treatment with the anti-ischemic drug ranolazine

summary: Heart failure is a leading cause of cardiovascular mortality with limited options for treatment. We analyzed whether the anti-ischemic drug ranolazine could retard the progression of heart failure in an experimental model of heart failure induced by 6 months of chronic pressure overload. The study showed that 2 months of ranolazine treatment improved cardiac function of aortic constricted C57BL/6J (B6)  mice with symptoms of heart failure as assessed by echocardiography. The microarray gene expression study of heart tissue from failing hearts relative to ranolazine-treated and healthy control hearts identified heart failure-specific genes that were normalized during treatment with the anti-ischemic drug ranolazine.

overall_design: Microarray gene expression profiling was performed with heart tissue isolated from three study groups: (i) untreated 10 month-old C57BL/6J (B6) mice with heart failure induced by 6 months of abdominal aortic constriction (AAC), (ii) 10 month-old B6 mice with 6 months of AAC and two months of treatment with the anti-ischemic drug ranolazine (200 mg/kg), and (iii) age-matched, untreated, sham-operated B6 control mice.


title: Expression and mRNA half-life data of acid and alkaline shocked Staphylococcus aureus

status: Public on Oct 01 2010

city: Omaha

first: Paul

last: Dunman

state: NE

address: 986495 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary: Staphylococcus aureus is a leading cause of hospital- and community-associated infections.  The organism’s ability to cause disease can, in part, be attributable to its ability to adapt to otherwise deleterious host-associated stresses.  Like other bacterial species, the modulation of mRNA turnover appears to play an important role in S. aureus adaptation to certain environmental stresses.  In the current study Affymetrix GeneChips® were used to examine the S. aureus responses to acid and alkaline shock-inducing conditions and to assess whether stress dependent changes in mRNA turnover are likely to facilitate the organism’s ability to tolerate extreme pH challenge.  Results indicate that S. aureus adapts to pH shock by eliciting responses expected of organisms coping with pH alteration, including neutralizing cellular internal pH, DNA repair, amino acid biosynthesis and virulence factor expression.  Further, it was found that the cellular response to alkaline conditions elicits a transcriptional profile that is similar to that of stringent response induced cells.  Consistent with that observation, we show that the activator of the stringent response, (p)ppGpp, levels are profoundly elevated during alkaline shock conditions.  We also show that the mRNA turnover properties of acid or alkaline shocked cells significantly differ from that of cells grown at neutral pH.  A comparison of the mRNA degradation properties of transcripts whose titers either increased or decreased in response to sudden pH change revealed that alterations in mRNA degradation may, in part, account for the changes in the mRNA levels of factors predicted to mediate pH tolerance.  Finally, a set of small stable RNA molecules were induced in response to acid or alkaline shock conditions.  As in other organisms, these molecules may mediate mRNA stability and adaptation to otherwise deleterious growth conditions.

overall_design: Staphylococcus aureus strain UAMS-1 was grown to exponential phase and either mock treated (pH maintained at 7.4) or subjected to acid (pH 4)- or alkaline (pH 10) conditions for 30 min.  Next, 200 micrograms per ml of rifampicin were added to arrest transcript synthesis.  RNA was extracted from cell suspensions at 0, 2.5, 5, 15, and 30 min post-transcriptional arrest, labeled and hybridized to S. aureus GeneChips.  A comparison of 0 min samples allowed assessment of acid and alkaline shock responses.  A comparison of 0 min to that of various post-transcriptional arrest RNA samples allowed assessment of the mRNA turnover properties of mock vs acid or alkaline shocked cells.  Duplicates of each experimental condition and corresponding post-transcriptional arrest time point were used (biological replicates).

first: Kelsi

last: Anderson

first: Christelle

last: Roux

first: Matthew

middle: W

last: Olson

first: Thanh

last: Luong

first: Chia

middle: Y

last: Lee

first: Robert